The Mercy Seat
by Alekto
Summary: COMPLETE Sometimes the Atlantis Expedition's attempts to understand the Ancients' technology work, sometimes they don't and sometimes things go really badly wrong. This is mainly a McKay and Sheppard fic, though some of the others do feature.
1. Teaser

**The Mercy Seat**

By Alekto

Rating: PG-13 or T

Genre: Action/Adventure with some gratuitous h/c thrown in.

Warnings: none.

Season/Spoilers: After Hotzone, but before Siege, so sometime late Season 1.

Summary: Sometimes the Atlantis Expedition's attempts to understand the Ancients' technology work, sometimes they don't; and sometimes things go really badly wrong. This is mainly a McKay and Sheppard fic, though some of the others do feature.

Archive: SGAHC, Helio, Wraithbait. Others please ask.

Disclaimer: I don't own 'em. I'm just borrowing and I promise to give them back after I'm done, though perhaps a little the worse for wear.

Author's note: I've tried to keep this fairly close to canon, but as I started writing this back in Season 1 there is a slight divergence from canon in that I have Zelenka going offworld. However, in "Duet", it's stated that that is Zelenka's first trip offworld. Also, for the record: I'm English, and so is the spelling.

Huge thanks are due to Susan Zell for her encouragement and comments, and likewise to NotTasha for the excellent job she did of beta reading. Any mistakes left are all mine.

o0o

**Teaser**

"Nothing's happening, Rodney," ground out Sheppard, an unmistakeable edge of urgency in his voice.

"Not really too surprising. No one's used this thing in thousands of years," McKay rasped, coughing painfully in the foul, leaden air, the exhalation condensing into billowing clouds in damp bone-numbing chill. "And God alone knows how much of that time it's been underwater," he muttered almost as an afterthought.

Sheppard remained where he was, laid back in the reclined throne-like Chair, his hands resting on the wide arms, just as he had done once before – admittedly by accident on that occasion – back in Antarctica. This time however, the Chair was most definitely not co-operating. Even through the BDUs he wore, he could feel the cold of whatever metal the Chair was made from leeching away the scant warmth in his body. A loud clang coming from behind and to one side of the chair's bulk startled him and he twisted around abruptly, only to find McKay had dropped the panel he had pulled away to gain access to the interior in an attempt to discover what was stopping it from working.

The latter fumbled for a few minutes, blowing on cold numbed hands in an effort to get some feeling back into them, then paused and peered about abruptly from where he was crouched, the partially teased out tangle of cables and crystalline blocks running to the chair temporarily forgotten. "What was that?" he whispered urgently, scoping out the room as if he had not seen it properly before. The sudden movement nudged the headache he had been nursing to new levels. "Major? I _told_ you before. There's definitely something down here."

He reached down to the Beretta holstered at his hip, heard the nearby click of a P-90's safety being disengaged, and felt rather than saw Sheppard's gaze tracking his own, checking out the room then staring back down the dank corridor they had emerged from only minutes before. The vestigial blue tinged lighting that had survived the ages in the domed room did little to dispel the pervasive murk. "I don't see anything," Sheppard admitted quietly.

"You sure?" The doubt in his tone was clear. "It's probably hiding… waiting to leap out on us when we least expect it. God! I'm talking like we're in one of those appalling teen slasher movies: dim lighting, a couple of poor brainless idiots wandering around with flashlights, something slimy with huge teeth lurking in the dark…" McKay's brittle laughter did little to reassure his team-mate.

Sheppard levered himself upward, ruthlessly choking back the pained gasp the movement caused and peered again into the darkness. Like spokes of a wheel spreading out from the hub, the empty corridors stretched away. In the dark, beyond the range of their flashlights he could just make out the faint shimmers of phosphorescence that outlined their own footprints along the corridor they had come down tracking through the stinking ankle deep mud. The only sounds were the almost imperceptible drone of the Naquada generator they brought with them on standby and the slow, unending drip… drip… drip… echoing from far off.

They could not even hear the warble of the City's alarm any more. The absence left a strange gap after its being part of the soundscape for so long, but they were too deep now.

Time crawled by as they watched and waited. "There's nothing out there," Sheppard finally decided and carefully settled back into the chair, only too aware of the stabbing ache in his side.

McKay harrumphed, gave one last, dubious, look down the corridor but trusting the Major's conclusion he knelt to return his attention to the task at hand.

He was too preoccupied to notice when Sheppard's gaze was drawn inexorably back to the surrounding corridors or the worried frown that slowly crept over his face.

o0o


	2. Chapter 1

**A/N: **Fanficaddict, Dragonfairymaiden, LTwill, Dr.Dredd, Jules47, angw, Robyn, MacCartney, Rowana Farrin, Crockett, Drufan, and puddles1311 - thank you all so much for the reviews so far.

FYI This fic has been completed and comprises 12 chapters (not counting the Teaser). Assuming I can get access to a computer, I will be updating twice a week from now on.

**

* * *

****Chapter 1**

_**30 hours earlier…**_

The decorous chiming of Atlantis' alarm system as always drew everyone's attention from their tasks. "Incoming wormhole!" came the shouted warning as lights flickered around the ring of the Stargate, settling on various of the symbols marked on it.

Doctor Elizabeth Weir turned sharply, surprised at Grodin's call. A brief check of her watch confirmed what she already knew: they currently had three teams on other worlds for various reasons, and none were due back for several hours yet. Even as she looked up the familiar liquid whoosh of an establishing wormhole settled to leave a gently rippling blue surface. "Activate the Shield," she ordered tersely, moving over to Grodin's desk as the latter swiftly pressed the appropriate symbol. Below them a barrier flared into life across the Stargate's surface while a squad of heavily armed marines took up defensive positions around the Gate. Through long habit she cast her eye around the Control Room, memorising the personnel on duty and noted the sudden presence of Doctor Rodney McKay taking the seat at a nearby computer to check incoming signals through the Gate. "Got anything?" she asked.

"IDC being received now. It's Frankel's team," he announced without elaboration.

"Lower the Shield," she said with forced calm. During her brief tenure at the SGC she had quickly learned that the early return of an off-world team usually meant the worst. Half dreading the reply she might receive, she spoke into the headset she wore. "Lieutenant Frankel, what's your status?"

"We've found something in the wreckage of the ship that was sending the distress signal picked up by the MALP," he began, the excitement in his tone clear even through the static in the transmission. "We can't be sure: I for one have never seen anything like it, but Doctor Zelenka checked it over and he thinks it might be some sort of power source. He's managed to disconnect it from the wreckage and it appears to have gone inactive. Zelenka wants to bring it back to work on."

"What is it?" cut in McKay's suddenly interested voice.

Weir hid a grin. Since spraining his ankle after a high speed, nick-of-time dive through the Stargate escaping some less than friendly locals on a planet visited by Sheppard's team a few days earlier, McKay had been hobbling around on crutches and generally feeling miserable. It had only got worse when earlier in the day Sheppard, Ford and Teyla had been obliged to leave him back on Atlantis while they went offworld on a milk run to pick up some much needed supplies. In the hours since they had left, McKay had moped around the Control Room, desultorily checking systems, fiddling with the settings on some of the computers that were hooked up to their Atlantean counterparts and generally annoying the hell out of the people stationed there.

Had anyone accused him of being worried for his team-mates, he would have laughed it off, tossed in a sarcastic comeback for good measure, and returned to his aimless tinkering while he waited for their safe return.

"Doctor McKay!" exclaimed Zelenka's surprised voice, "I thought you were off duty? Ah, never mind. I think this is a very interesting thing we have found," he continued, his accent thickening in his excitement. "I am hoping to tell you more later, but initial tests show it has potential power output much greater than our Naquada generators, though unfortunately nothing like a ZPM. Perhaps with more testing I think it might be possible that we can adapt it to use with our equipment."

"Any idea of how it works?" asked McKay, an eager expression on his face, the misery of the previous hours swept aside as his mind latched on to a tantalising new puzzle.

"Hold it, you two," interrupted Weir before the two scientists could get too involved in their debate. As fascinating, not to mention useful, as it all sounded, she had a more pressing concern. "Lieutenant Frankel, Doctor Zelenka, do you think it's safe to bring this device back to Atlantis?"

There was a moment's pause before Frankel replied, "Ma'am, I can't see anything that looks obviously like a threat or a security device, but like I said, this thing is way beyond anything I've seen before, and that includes what I've seen of the stuff the Goa'uld use."

"I agree, Doctor Weir," added Zelenka, "we cannot be sure without much more investigation, and for such investigation we must bring it back to Atlantis. To bring such an object back is a risk, yes, but if the readings I've been getting from it and the preliminary calculations I've made are correct, I think there is the potential that it may have sufficient power to at least partially activate the City's main defensive shield."

Weir glanced over to McKay. "Sounds like it might be useful," he grinned, the discomfort from a sprained ankle temporarily forgotten in his impatience to start checking over some bit of unknown technology.

She nodded slowly. "Alright, lieutenant, bring it back. Rodney, put a team together to start working on it, but be careful! If it has the kind of power output Zelenka says…."

"Don't worry, Elizabeth," McKay brushing aside her concerns with characteristically blithe confidence, "I have no intention whatsoever of blowing myself up."

A few minutes later Lieutenant Frankel's team emerged from the gate, balancing between them something the size of a large steamer chest on the back of the cart.

o0o

"Ah ha!" crowed McKay triumphantly as a low, almost subsonic, thrum of power began reverberating through the laboratory. At a nearby workstation Zelenka, who was using one of the laptops the expedition had brought through with them to monitor the Canadian's progress, looked up with a matching grin. Others of the scientific team were stationed around the lab, making their own observations, glancing occasionally at McKay as the readouts they were tracking hiccupped or wavered through nothing more than, each hoped, his ceaseless fiddling with the device's settings.

"How's that?" asked McKay as he made a few more tiny adjustments.

"No better than the last two dozen times. As before, I am reading considerable _potential_ here, much as I observed on the planet, and indeed, much as we have seen while we have been working on it so far," the Czech replied after watching the computer readouts for a couple of seconds, "but still we are not managing to create measurable power output."

McKay frowned in annoyance, sighed, and experimentally flicked one of the many switches on the device to and fro a couple of times. Getting no reaction from the monitoring scientists, he walked over to peer over Zelenka's shoulder at the readouts, favouring his ankle as he did. With scant regard for the Czech's presence, he reached past him for the keyboard and started toggling through the records of displays and readouts they had amassed over the previous hours of work, pausing here and there to double check settings.

"Doctor, so far it's behaved differently from any other power source we've seen," ventured another of the team. "Perhaps it's our set up that's at fault. We've been working on the assumption that it's functioning broadly parallels other power sources we're familiar with. If that initial assumption's incorrect, maybe we've just got the connections wrong?"

"Well, naturally," groused McKay, "why don't we all take everything apart and put it all back together again in a different order." Acid sarcasm leeched into his voice. "Here I am surrounded by people who are _alleged_ to be amongst the top scientific minds in their fields and the best idea anyone's come up with so far boils down to 'let's switch a few wires around and see if it works then'. Why on earth should we want to use any different technique to connect up an alien power generator than mimic what most idiots do when they're trying to get their DVD player to work?"

An embarrassed silence settled over the laboratory. McKay looked at Zelenka who shrugged and offered an apologetic half smile. "It couldn't hurt, could it, Rodney?"

McKay sighed wearily, nodded in reluctant agreement and curtly yanked out a handful of the wires he had spent the previous hours connecting to the device.

Immediately they came loose, the formerly rhythmic, almost comforting low thrumming of power hiccupped and stuttered. Around the laboratory the smoothly curved wave patterns displayed on monitors leapt sharply, their arcs shattering into hard edged fractals. Laptops started chirruping alerts to users who were already frantically trying to work out what had happened. McKay looked around the lab, taking in the readouts. "Oh, definitely not good…" he muttered.

Above them, all but ignored amidst the growing hubbub, the familiar chiming of the City's alarm began to sound. Moments later a gently modulated, sepulchral voice started to intone something in a language some recognised but none understood. For a couple of seconds Zelenka tilted his head, listening but not understanding. Before returning his full attention to his work, he noted absently how the words had sounded oddly reminiscent of Mass.

Then Mass or anything else was suddenly the last thing on his mind as one after another, the laboratory's laptops and monitors crackled, smoked and exploded, filling the air with the acrid stink of burning plastic. The monitor on his own machine flared white, and when he saw thin plumes of smoke rising from the keyboard he stumbled backwards, overbalanced and fell.

"Do prdele!" the Czech swore from his sprawled position on the floor.

o0o


	3. Chapter 2

**Chapter 2**

In the Control Room the technicians on duty looked from one to the other as the alarm began before returning their attention to the screens of the laptops hooked into the Atlantis mainframe in search of what had set off the alarm.

Peter Grodin studied the display on the console in front of him and frowned. He tapped in instructions on the laptop connect to the console, waited, swore quietly, tapped in more instructions then swore again, less concerned this time about being overheard. While he watched, Atlantean glyphs started to overwrite the English characters on his laptop's screen.

Elizabeth Weir looked at the main screen in the Control Room, frowned as the plan of the City displayed there winked out and was replaced by column after column of Atlantean code tracking across the screen, too fast to read.

Andrew Baines saw the diagnostic programme he had been running abort, then crash altogether. He was looking towards Grodin and Weir for instructions when the jack connecting his computer to the mainframe exploded in a fountain of sparks.

Around the Control Room connection hubs smoked and failed. Scientists leapt backwards as the equipment they had been working likewise burned or exploded. Energy crackled around suddenly exposed power cables. The sharp tang of ozone and the more acrid stench of burnt plastic filled the air. Behind the hubbub, the alarm warbled on as, unnoticed by the people in the control room, an incongruously calm voice intoned alien words.

"Talk to me, Peter!" called Weir, fighting to be heard over the chaos. "What's happening?" Around the rest of the Control Room cries for help and medical assistance merely added to the din.

Grodin looked up at her, his face smudged with soot from the smoke billowing from the burning remains of his own computer. "I don't know!" he shouted back. "Some sort of power surge maybe. Whatever it was, it must've been huge! It's blown straight through the surge protection we have installed." He was about to go on when the familiar sound of the Gate Shield being activated drew everyone's attention to the presently inactive Stargate.

"Did you…?" asked Weir.

Grodin shook his head, slid his chair over to the Gate's control console and pressed the deactivation key. He looked up to see the shield still in place, leaned back over the console and tried other buttons but all to no avail. "None of the controls are responding, Doctor," he reported redundantly, before kicking his chair over to another console. "The same thing here. It's dead."

Other voices rang out. "The City's communications grid is down!"

"Internal monitoring is offline!"

"All secondary controls are unresponsive!"

"Everyone calm down!" ordered Weir firmly and a slowly a semblance of quiet descended over the room. "Concentrate on assessing the damage to your own stations. Someone get on the radio and get what people up here you need. I'll want a preliminary status report in fifteen minutes!"

Muttered affirmatives were the only response as those able to tried to work out the extent of the damage. Minutes passed, Weir looking over Grodin's shoulder as he ran through permutation after permutation on the main control panel, before deciding that it was as inert as the rest.

Out of the corner of her eye Weir glimpsed an approaching figure and looked up at the cautious approach of a woman whom she recognised as the linguist attached to the scientific team and who she knew had not been on duty in the Control Room. "Doctor Meidani," Weir greeted brusquely. Since their arrival, she had seen little of her. Leila Meidani had not been on Weir's initial short list for the Atlantis expedition, but both the linguists she had approached for the expedition had demurred and recommended, amongst others, the Iranian born Meidani. After checking her academic credentials, Weir had gone along with their suggestion. The reaction to her selection from the people running the security checks on the expedition members had been interesting, to say the least.

"Doctor Weir," Meidani returned with a brisk nod of greeting. The Iranian was about Weir's age, though less tall, her long black hair tied back in a severe ponytail. She went on, speaking with only the barest hint of a Middle Eastern accent. "I was wondering if you have been listening to the city's automated announcement?"

Despite the polite words, Weir could not help but hear the urgency in her tone. Closer scrutiny revealed the worry in the face of the normally unflappable Iranian, and for the first time since the crisis began, she directed her full attention to the announcement. She was, she freely acknowledged, much better with the written rather than the spoken form of the language, but even so as she listened she could understand enough to appreciate Meidani's concern. Their eyes met, and Meidani caught the request implicit in them. She began speaking, softly enough not to be overheard, but murmuring for Weir's benefit a running translation from the Atlantean. "Attention! Attention! This is a security announcement. The presence of an unauthorised active alien power signature has been identified within sector 3-182-76. Detected power output has exceeded permitted limits and has been classified as a level two threat. Standard security protocols have now been implemented. I repeat, standard security protocols have now been implemented: all personnel should report to assigned stations immediately. Atlantis is now operating at level two security."

As the Iranian woman finished speaking, Weir caught sight of the approach of her two top computer experts, Baines and Grodin. Meidani saw the seriousness in their expressions, murmured her excuses and moved away, leaving Weir to take their report in private. "As far as we've been able to determine, all external links we set up between our computers and the Atlantis mainframe have been broken," explained Grodin. "I can't be sure, but it's looking like there's been some kind of huge feedback or surge across the whole system. Atlantis' own secondary controls went down the same time and are still inactive. As best we can tell, all primary systems are functioning, but so far we've been unable to re-establish access."

"There's been a significant amount of damage to every computer that we had hooked up to the City when the surge hit," Baines continued, "and those that weren't physically damaged seem to have been infected with a virus that's overwriting any data on the hard drives. My maintenance team can salvage some of them and we'll have to cannibalise others for spares, but the bottom line is it'll take time and we'll still be down a _lot_ of machines."

Weir nodded: she had expected worse. "Do your best," she said with a tight smile of encouragement.

Baines headed away leaving Grodin with Weir. "We still haven't been able to access the controls of the Gate or the Gate Shield," he reported. "I've tried everything I could think of. Although Atlantis' primary systems such as the Gate controls and the Shield are, in fact, fully operational, the computer refuses to accept any instructions from us. Doctor Weir, Major Sheppard's team is due back in a little over two hours. Without being able to dial out, we've no way to contact him, to warn him. We've even thought of trying to get to a Puddle Jumper to use their on board systems to access the Gate, but bulkheads have come down blocking access to the hangar, and we've no way of knowing if we would be locked out of their controls as well. If the Major tries to come through…" Grodin's words tapered off. Both knew only too well what the result would be.

Weir sighed, closing her eyes as the once overheard morbid humour of a technician back at the SGC sprang unwanted into her mind. _Bug on a windshield._

She opened her eyes, mouth set in a determined line._ Not on her watch!_

"Get McKay up here!" she ordered.

o0o


	4. Chapter 3

**Chapter 3**

A flustered McKay hobbled into the control room, his crutches abandoned while working on the alien generator for a more manageable cane.

"Rodney, we've got a problem," Weir began without preamble.

"I'm well aware of that," McKay snapped back without breaking pace as he stormed towards her. "It turns out that the interesting new power source Zelenka found for us isn't exactly what you'd call stable. So unless whatever's going on here is of truly overwhelming importance, I'm going straight back there to stop the thing overloading anything else or melting down and taking us all with it!" He paused in his tirade, finally taking in the devastation in the control room and the active gate shield. The righteous certainty ebbed from his face. "Uh… what's happened here?"

In terse sentences, Weir filled him in.

McKay nodded slowly and looked around. He caught sight of one of the technicians who had been on duty in the control room. "Hey!" He clicked his fingers to get his attention while struggling and failing to recall the man's name. "You!" he continued. "Get in contact with Doctor Zelenka. Tell him he needs to make sure that generator he's working on gets fully shut down right now!" The man paused, glancing to Weir for confirmation. "Sometime today would be good if you can manage it!" McKay added in a sarcastic drawl. The technician nodded once and fled.

With that accomplished, McKay walked the control room, stopping here and there to examine areas of damage or to question some of the growing crowd of people Weir had pulled in who were engaged in assessing the extent of the repairs that would be needed. Doctor Carson Beckett and his emergency team were still working on getting the worst of the injured ready to be taken to sickbay, while the handful of marines trained as medics were ably offering first aid to the less seriously wounded.

Five minutes later McKay ended up back with Weir at the main control desk, one of the few intact laptops tucked under one arm. Standing in discussion with Weir was a squat, middle-aged man with a Union Jack shoulder patch. A second man, taller and younger but also sporting the British flag on his jacket stood beside him. "Rodney, you've met two of our engineering team, Captain Roberts and Sergeant Callaghan haven't you?" said Weir covering for the Canadian's occasional inability to correctly remember names.

McKay gave them a cursory once over and promptly ignored them. "Elizabeth, in the time we've got before the first off-world team's due back, I don't have time to even begin to finesse a solution to what's happened to the computers. We need to get the Gate Shield down and we need to do it fast. I've got a schematic of the main power routing in the Control Room." McKay unfolded the laptop and brought up the requisite diagram. Roberts moved closer to study it. "We were lucky: it was one of the things we'd downloaded a while back to work through, and it was on a computer that wasn't hooked up to the city when everything went crazy."

Roberts' stubby finger started tracing the power routing lines on the diagram, pausing here and there to scribble details down in a small notebook. McKay watched him for a few minutes, peering over at his notations, back to the screen and grimaced. "No, no, no, no…" he slapped Roberts' hand from the laptop, pulled over the notepad and started writing over Roberts' pencil scrawl in biro. "_That_ goes _there_, and connects up with _that_!"

"That's not what the schematic says…" began Roberts slowly.

"Then it's wrong!" McKay interrupted, then went on cuttingly. "Where did you learn engineering theory? Watching reruns of Bob The Builder?"

"Not quite," Roberts replied mildly in a broad, phlegmatic Midlands accent. "Doctorate in engineering from Imperial College, London, since then fifteen years with the Royal Army Ordnance Corps, and more recently the Royal Engineers."

McKay looked at him as if seeing him for the first time: military grunts with doctorates was a concept that really did not fit into his worldview – with the notable exception of certain very attractive blonde astrophysicist lieutenant-colonel… But then looked at Roberts, smirked slightly and went on, "so, fill me in on how much experience have you had with Stargate mechanics?"

"Not too much," Roberts sighed. "I'll defer to your expertise there, Doctor."

"Right!" McKay smirked, satisfied that he had re-established the intellectual primacy of the scientific side of the expedition. "So whose information are you going to trust? Mine or the computer's?"

Roberts said nothing, but from behind he heard in a soft muttered Northumberland burr, "is that a trick question?" When he turned to reprimand his sergeant, Callaghan was already walking away towards Baines and Grodin standing at another console. A glance at McKay showed the Canadian seemed to have been utterly oblivious to the comment, deeply engaged in amending and expanding his notes.

A little under an hour later, laden with scrawled notes and diagrams set out on both McKay's laptop and Roberts' notebook, the two were reporting to Weir with their conclusions. Before Roberts had time to even manage a greeting, McKay announced peremptorily, "I know how to deactivate the Gate Shield."

Roberts raised an eyebrow a little at the 'I', but let it go. Being honest with himself, he recognised that a good 80 of the input into the plan they had come up with had been down to McKay. He had merely streamlined and tidied up aspects of the implementation – that was when he hadn't been struggling to keep up with the astrophysicist's thought processes. The man was without doubt a genius, but not for the first time did he catch himself wondering how Major Sheppard had managed to put up with him as long as he had.

"Since we can't shut down the Gate Shield using the controls, the best alternative we've been able to come up with is to manually disconnect the power from the Shield." McKay pulled up a schematic on the laptop and turned it to face Weir. "This is the route of the main power cable to the Gate," he indicated, "supplying both the Gate Shield and acting as a power regulator for the Gate itself, which as you know is largely independent of the city's power source… except of course when it needs to be boosted by a ZPM to enable intergalactic travel. If we disconnect that, it should automatically divert to the back ups. Those are more difficult to access, but we think we've located the routing for the gate shield back up power supply, so if we cut that too, it will deactivate the shield, but leave other gate functions intact and running on their own back up."

Weir looked at the plans and schematics then at McKay. "From this it looks like you'll need to cut through these layers of ducting to get to the power cables. Do we have the equipment to do that and disconnect both power supplies before Major Sheppard's team is due back?" she asked.

McKay winced slightly and looked over at Roberts. "Uh… not quite… um, that's to say we _can_ cut through to them, but…"

"Rodney!" Weir said warningly, "what is it you're not telling me here?"

McKay opened his mouth to speak, but the engineer pre-empted him. "We don't have access to the kind of equipment we would need to do it quickly, and the cutting tools we do have access to here won't be able to cut through both the ducting and the power cables in the required time frame," Roberts explained calmly. "In my opinion the only reliable way that we're going to be able to disrupt the power supply to the Gate Shield before the Major's team is due back is to use explosives to break the connections."

"So you're saying in effect, we're sabotaging the Gate Shield?"

Roberts straightened to a parade brace. "Yes, ma'am, I'm afraid that's exactly what I'm saying."

"How repairable is this bit of sabotage likely to be?" Weir asked. "Assuming we get through this, there's no question we're still going to need to be able to use the Gate Shield."

"If we just get the power cable, we can replace the damaged length using redundant material from elsewhere in the City. It would most likely take a few hours; a day at the outside. If there's more collateral damage than we're predicting… that might make things a little more difficult," Roberts admitted.

Before he could say anything more, McKay cut in sharply, "yes, right, whatever, but right now we need to get the Shield down and Sheppard's team and the others safely back!"

Weir nodded slowly. "So the bottom line is we have to sabotage the City ourselves? This is the only viable option we have?" She glanced over at McKay who grimaced slightly at the terminology but did not contradict the appraisal. "Set it up," she ordered.

o0o


	5. Chapter 4

**Chapter 4**

Looking around the once pristine gate control room Weir had to admit that the place looked like a bomb had hit it, then her mind caught up with the incongruity of the thought and she choked back the entirely inappropriate smile. Captain Roberts and Sergeant Callaghan, along with some of the marines with demolitions experience, had rigged shaped explosive charges at strategic points along the walls of the Gate Room. McKay was hobbling around, PDA in one hand, cane in the other checking and double checking their locations between frequent glances at his watch: Sheppard and his team were due back in less than thirty minutes.

"We're nearly done. Final checks, people!" called out Roberts. "Everyone who doesn't need to be here, clear out now, please!"

Technicians and scientists who had been trying to repair the damage done by the earlier surge shut down their work and left. Within minutes the only people in the gate control room were Weir, Grodin, McKay and Roberts' demolitions crew. Then Sergeants Bates and Callaghan reported their readiness and everyone started moving to the shelter offered by the rear section of the observation deck overlooking the Gate. On his way to the staircase Callaghan handed his CO the remote detonator.

Less than half the marines had vacated the area when everyone heard the unmistakeable sound of the Stargate started to dial up. Lights flickered around the outer ring and settled on the first chevron. Slowed by his twisted ankle, McKay was still on the stairway to the upper level as the Gate started to activate. Roberts looked down with a frown at the countdown on his watch which was still reading seventeen minutes to Sheppard's scheduled return. "Bloody American pillock's early!" he swore, then calling out more loudly. "Get clear! I might have to set the charges off early. Everyone hunt cover!" The others followed his instructions as he hurriedly keyed the correct frequencies into the remote detonator that would set off both charges. A snatched glance upward showed McKay still on the main staircase, dithering between finding cover and trying to figure out how to help. "McKay, that includes you," he yelled. Just as he finished keying in the last series of digits, the final symbol on the gate illuminated and locked. The familiar fluid 'kawoosh' of the establishing wormhole was blocked by the still active Shield.

For an instant everything paused. Then from above he heard a voice calling out, "receiving Major Sheppard's IDC!"

Roberts looked at the explosives no more than twenty feet away from him, then at the staircase leading to the upper level - too far to reach in the few seconds before Sheppard would surely try to come through the Gate. A few feet away he noticed one of the heavy packing cases brought from Earth, weighty in itself, and still half full of gear that had been moved in to supply the repair effort. He was hardly aware of the moment when he made the decision, but even as he was throwing himself behind the scant cover it offered, little more than a second after hearing confirmation of Sheppard's IDC, he yelled, "GET DOWN!" and activated the remote detonator. Out of the corner of his eye he saw an instant's appalled shock on McKay's face before he too dropped where he was on the wide landing half way up the main staircase.

The roars from the two explosions came so close together as to be almost indistinguishable. The charges might have been shaped, but the volume of explosive required to be sure of penetrating the ducting and severing the power supply was such that even the spacious Gate Room was confined enough that the severity of the concussion blast took most people by surprise. Many of those on the upper floor who had not had time to reach shelter were thrown from their feet, though apart from cuts and bruises not badly hurt.

Roberts however had not been so fortunate. He had known he was perilously close to the explosives, but before he was able to hunker down behind the packing case the blast had caught him and flung him against one of the support pillars. The last thing he saw before the greyness encroaching on his consciousness swept over him was the flicker of the Gate Shield going down.

No more than five seconds later Major Sheppard, Lieutenant Ford and Teyla Emmagan emerged from the event horizon into Atlantis' Control Room to a scene far different from the one they had left.

Sheppard stopped a few feet from the Gate and looked around. Coils of smoke snaked towards the ceiling and spread out across it in dark billows. The air was foul with the smell of cordite, burnt plastic and a definite, if faint, tang of ozone. A squad of US marines, bizarrely preceded by a British Sergeant hastened down the main stairs. Some stopped to help a grimy, coughing Rodney McKay to his feet while others continued on towards a supine form lying next to the base of a pillar. From the upper level he heard Weir's voice urgently calling for a medical team to be sent to the Control Room.

"What the hell just happened?" he asked no one in particular.

Anyone in earshot seemed too preoccupied to answer, but he saw Weir heading down to meet him. She paused on the way, taking a few seconds to confirm that beyond a few comparatively minor cuts from flying debris, McKay had not been badly hurt by the explosions. Even he seemed relieved that their self inflicted sabotage had worked, to the extent that temporarily at least the handful of cuts on his face and arms were forgotten. He appeared content to sit on the stairs and wave a greeting to Sheppard while one of Beckett's team cleaned and taped his cuts.

Picking her way over the scattered fragments of architecture, Weir made her way to where Sheppard was still stood next to the now inert Stargate. "Good to have you back safe, John," she smiled warmly.

He looked at her, saw the smudges of grime on her face and clothing, saw the tension in her stance. Before he could reply, the timbre of the city's alarm altered, and a finely modulated voice commenced speaking in a language the recently returned Major only half recognised.

Weir, however, recognised it all too well. And even as she welcomed the safe return of expedition's military commander, she was just able to understand from the computer's emotionless warning that an attack had been registered in the Gate Control Room and grimly wondered what further problems a 'level four' security condition would entail.

o0o


	6. Chapter 5

**Chapter 5**

Weir looked around the unusually full conference room and forced a confident smile. The events of the past day had shaken her people more than most cared to show, but she knew them well enough to read the signs. They had all become too complacent, too comfortable with thinking of this alien city as a safe refuge; thinking of it as home. And now, it seemed, they were paying for their arrogance.

Her core group of advisors and experts had been joined by some of the specialists in the military contingent as well as representatives of the many scientific disciplines. All looked tired. Since the alarm had been triggered some twelve hours before, they had had little opportunity for sleep, but at last all her people, including those who had been offworld, were accounted for. Some sported bandages, and there were few there whose clothes were not darkened by dirt and soot. Captain Roberts hobbled in last under Beckett's disapproving gaze. Sheppard's renowned aversion to spending anything more than the absolute minimum of time in the infirmary seemed to be catching, mused the Scot. The plaster cast on Roberts' broken leg had barely set when the engineer insisted on attending Weir's briefing, but given that a broken leg and a mild concussion were the worst the British engineer had suffered, no one would dispute that under the circumstances he had got off lightly.

"Now that we're all here," she began, nodding greeting at the late arrivals, "I need to be sure that everyone knows where we all stand. Most of you know what happened, but to sum up: at 2043 hours yesterday the City's internal sensor net detected an energy signature that it identified as a threat and activated an automatic response. At that point any non-Atlantean technology that was interfaced with the City's mainframe was attacked and the connection severed. All external access points, including all access to the Puddle Jumper bay, were shut down and the defensive shield across the Stargate was activated. The automated announcement described this as a 'level two security' condition."

"However, since Doctor McKay and Captain Roberts were forced to destroy the power conduits leading to the Gate Shield as the only way to bring it down and allow the teams we had offworld to return safely, the security condition has now advanced to 'level four'."

"Do we have any information yet on what this level four security condition means in practical terms?" Sergeant Bates asked.

Weir sighed. "Under ordinary circumstances we could check the City's computer database, but obviously at the moment we're locked out so we can't be entirely sure. In addition to our current inability to access the Atlantis mainframe, it seems that a number of bulkheads have come down in some parts of the city and the internal transport system isn't working, but beyond that… Doctors Grodin and Baines have been trying to get into the main control system, but so far without success."

"We're not going to get far looking at symptoms," McKay announced peremptorily. "I happen to think the solution's much more straightforward than pulling computers apart and trying to rebuild them. If I'm right, the Ancient gene itself might be the key to bypassing the lockdown."

Grodin shook his head. "I'm not sure how you figure that, Rodney. Andrew here," he pointed at Baines, "he's had Beckett's gene therapy and it doesn't seem to have made any difference with trying to get the computer to respond."

"Yes, but that's the gene _therapy_. It may be possible that at higher degrees of sensitivity the scanners in Ancient technology may be able to distinguish between the ATA gene therapy and the original. Hasn't anyone else thought it odd that the infirmary is one of the few places where things are mostly still functioning?"

The shrugs and blank looks gave him his answer. McKay rolled his eyes in despair at the Scotsman's apparent lack of interest in scientific observation. Beckett looked from him to Weir in time to see the accusation in her gaze and he shrugged self-consciously. "We've been a wee bit busy these past few hours," he hedged. "To be honest, I've just been glad things _were_ working."

The impatience ebbed from Weir's eyes as quickly as it had arisen as she saw the exhaustion in her Chief Medical Officer's face. With the injuries his staff had been handling since the crisis began, she knew he and his staff were managing on even less rest than she. Weir looked back at the physicist, following his line of reasoning through its logical conclusion. "Okay, Rodney, I'm assuming by this point you've talked Major Sheppard through what he needs to do to return computer access to us."

"Yes, well… uh… not exactly. I took the liberty of mentioning this to the Major a bit earlier and he's already tried to cancel the alert but it didn't quite seem to work out that way."

"Rodney…" Weir tried to hide her exasperation. She had learned early on in their acquaintance that when McKay had an idea, the niceties of team work – such as keeping the team leader informed of his intentions – had an irritating tendency to get omitted.

"Hey! The computer responded to him, allowed him access... of sorts," blurted McKay defensively. Success, he had long ago discovered, was a good way of smoothing over any perceived lapses in protocol. The only thing was, this time he had to admit that his plan had not been entirely successful. "There's just one problem, it just wouldn't let him actually _alter _anything. Consider it as our having discovered a 'read only' setting."

"If nothing else, at least that means we can figure out what the various security levels mean," Bates mused aloud.

Weir nodded her agreement. "Good idea. See if you can get Doctor Meidani to..."

"Already underway," Sheppard nodded.

McKay looked at him,insulted. "What? My translations aren't good enough?"

"I wouldn't exactly say that, but at least _she_ usually translates into something resembling English…" the Major retorted.

"So, what are you saying my translations are… _exactly_?" McKay glowered.

"Gentlemen…" warned Weir, cutting off the argument even as she saw Sheppard about to reply, and reflecting that with those two she sometimes felt disturbingly like a Principal adjudicating a schoolyard argument.

The two looked at her, saw the tension and the weariness in her face, and mutely accepted the rebuke. "Okay," Sheppard said getting back down to business, "As I said,Doctor Meidani's already beengoing through what we've found on the database and this is what we've got so far. The computer's got a whole series of programmed responses in the way it reacts to certain events."

"Ah! Like what happened with the virus outbreak a couple of weeks back," Zelenka exclaimed.

"Exactly," Sheppard said quickly, forestalling McKay's interruption. "It's set up to react with different responses to different perceived threats."

"And in its infinite wisdom it seems it's decided to categorise Doctor Zelenka's most recent bit of duty free as an hostile incursion," McKay continued, taking over the explanation without a pause.

"Hang on!" said Roberts. "Since the ZPMs are all but depleted, the computer's drawing power from our own Naquada generators, so why can't we just disconnect them and shut down the computer's power supply? Wouldn't that stop whatever anti-intruder programme it's got running?"

"A typically inelegant engineer's solution," sniffed McKay desultorily, "and, as it happens, with just a couple of problems. First, bulkheads have closed blocking off all access to the sites where the Naquada generators are located which would make getting to all of them to shut them down a very time consuming procedure. And second, unless you're suggesting we're all going to permanently move to the mainland and take up a new and exciting career in agriculture and land management, we'll need to reconnect the generators at some point to provide power to the City."

"And considering it's supposed to be a security measure, I suppose it's unlikely that cutting the power is likely to convince it whatever threat it was reacting to has gone," Roberts admitted to himself.

"So as it's responding to Zelenka's generator as a threat, we need to get it out of the city," concluded Weir. "If the Puddle Jumpers are still working and we can cut a way through to them, we can try using their onboard dial up to activate the gate, then mount the generator on a cart and send it back to where it came from." She looked at the faces of her team, her gaze slipping from McKay to Sheppard, Zelenka, Meidani and back to McKay. The grim set to their faces told her more eloquently than any words that it was not going to be that simple.

"We do need to get rid of the generator somehow, but at the moment that's only removing the cause, not the problem," the Canadian said wearily. "Perhaps if we were still at 'level two', getting rid of the generator would have been good enough, but given how far it's progressed now, the whole system needs to be reset and according to the stuff that Doctor Meidani's been translating, it's beginning to look like that can only be done using the Control Chair. And of course the problem is that without a ZPM, we don't have a power supply substantial enough to initialise it, let alone bring it fully on line. But that's not the worst of it. According to the database, now we've managed to hit level four on this incursion-o-meter the City's idiot computer is running off, we're really in trouble. If the system isn't reset or updated during a certain time, it proceeds automatically to the highest security condition: level five. The whole thing is designed as a failsafe: a final response to invasion."

"What does that mean exactly? That level five's a self destruct? Surely without a ZPM it won't have enough power to destroy the city!" Weir argued.

"And the Naquada generators we brought with us have their own built in cut outs to prevent their overloading. I know that the automatic safety cut out can be deactivated, but it can only be done manually," added Ford. "It can't be done by remote."

McKay looked around at them pityingly at their apparent lack of comprehension. "It won't take ZPMs or Naquada generators. Atlantis is floating in the middle of the ocean. All it has to do to get rid of us is to re-submerge the city and let the sea do the job for it."

"And according to the computer, the clock has already started," Sheppard finished quietly. "In a little under twenty hours, Atlantis returns to the deep."

o0o


	7. Chapter 6

Thanks as always for the reviews. They're much appreciated. And for anyone wondering, the relevance of the Teaser should become clearer in this chapter.

TheNaggingCube – Glad to hear you like Roberts. I figured the expedition needed another Brit or two. g>

Jules47 – 'Atlantis in deep trouble'. LOL

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**Chapter 6**

"In a little under twenty hours, Atlantis returns to the deep."

Sheppard's announcement was met with stunned silence. For long seconds the only sound to be heard was the gentle rush of waves breaking against the outside of the city as people looked from one to another in shock.

"We'll have to evacuate!" blurted Kavanagh. Some of the scientists sat nearby nodded their agreement. "Since we've no way of using the Chair to regain control over the City, it's the only logical course of action open to us," he went on, warming to his topic, looking around the room as if daring anyone to disagree, his eyes lingering warily on McKay and Sheppard. General muttering arose from all around the room as people started debating the pros and cons of Kavanagh's plan with their neighbours.

After a few seconds, Weir called for order and a reluctant silence settled once more. "Anyone else got anything constructive to say?" she asked, opening the floor for comments, but looking in particular at McKay and Zelenka who for their part seemed to be ignoring her entirely. They were sat alongside each other, sharing a laptop, both working at whatever was set up on it. The faces on the group able to look over their shoulders reflected equal parts interest and bemusement.

Before she could ask what they were doing, another voice cut in. "With all due respect to Doctor Kavanagh, I would like to suggest that there might be an alternative to evacuation." Leila Meidani looked at Kavanagh over the lid of an open laptop and then to Weir. "Contrary to expectation, there has been little to no call for a linguist during our meetings with the inhabitants of the Pegasus Galaxy." The Iranian's voice slipped into a lecturing tone. "It is such an extreme statistical improbability that all people should have evolved a language so similar to English that we can only theorise that the ability of people from so many worlds to communicate with each other must be a corollary of Stargate travel itself." She paused, noted the growing impatience on Weir's face and added hurriedly, "which is interesting but not immediately relevant."

"The point I am trying to make," she continued after a slight pause, "is that since the expected role of a linguist has proven unnecessary, I have been working with Doctors Baines and Grodin on putting together an automatic translation matrix for Ancient, something more comprehensive than the current system. As yet it's far from completed, but in working on it I have needed considerable written and spoken sample material of the Ancient language. For this I have been using some of the records from Atlantis' historical archive. In some of the earliest entries I have been accessing, there has been occasional mention of a Control Chair." She stopped and looked at Weir then around the room at the others watching her, slightly surprised as if expecting a more interested response to her statement. Then, as if realising her point had not been completely understood, she went on speaking by way of clarification: "_Another_ Control Chair."

Sudden discussion swelled around the room at the revelation. "And you hadn't decided to tell me about this earlier why exactly?" spat McKay in undisguised irritation as if the omission was a personal insult, his harsh, sarcastic tone cutting effortless through the noise. Weir might have been silent, but her own expression mirrored McKay's words.

"Until now, I did not think the information had any relevance," Meidani said with a contrite grimace. "My understanding was that the Chair we have cannot be used, so a second one was nothing more than a curiosity which was why I did not think it worth mention," she went on, offering an apologetic shrug as she did.

While she was speaking, Grodin reached over, pulled the laptop she had been using in front of him, started bringing up other windows displaying maps and schematics and started typing. McKay and Zelenka got up from their seats and joined him, speaking amongst themselves so quietly even those near them struggled to overhear. Wordlessly Meidani left her seat and just got out of their way.

After a few minutes the trio's whispered debate stilled and they looked up to find every eye in the conference room on them. "I think we have something here, Elizabeth," said McKay. "The data is somewhat limited, but it's looking like this other Chair appears to have a significantly lower power requirement to reach its activation threshold, perhaps low enough that one of our Naquada generators would be sufficient, but we'll need to run some power consumption equations to be sure."

Weir nodded but said nothing. Years of experience around the negotiating table had made her a fair judge of people, and she knew the trio from her scientific team needed no encouragement to find a solution. "Gentlemen," she began, waiting for a moment to be sure she had their attention, "I want a progress report in two hours." McKay did not even look up from his work, merely waved a hand in acknowledgement. "Meanwhile, we've got to plan for the worst case scenario," continued Weir. "Major Sheppard, Teyla, Sergeant Bates, I want you to come up with an evacuation plan should it become necessary for us to leave. Major Sheppard, arrange with Doctor Zelenka to get the alien power generator moved to the Control Room and mounted on a cart so we're in a position to get rid of it as soon as the Gate controls can be accessed. If anyone comes up with any ideas in the meantime, see me immediately, but otherwise just carry on with the repairs. Thank you everyone."

o0o

Five minutes later than the two hours she had specified McKay, Zelenka and Grodin pushed their way past the repair teams into Weir's office to find Sheppard finishing up briefing her on the evacuation plan. He made to leave, but Weir waved him to stay and he slouched in a chair to listen to McKay's report.

"This is what we've got," said McKay, flipping open a laptop and orienting it towards her. A series of complex equations filled the screen. "These relate to the power requirement for the Antarctica Chair. Based on the information we've gathered from the old records, these functions," he hi-lighted parts of the equations as he spoke, "have no equivalent in the secondary Chair referred to in the archive, so if we dispense with them, the power requirement is… so." The hi-lighted functions disappeared and a new equation appeared below. The three scientists stood around looking distinctly pleased with themselves.

Weir studied the equation, recognising only a few of the mathematical symbols alongside the Greek and Cyrillic letters, but having little idea of what they might represent. "Your conclusions?" she prompted.

McKay looked at her, a slight frown on his face as if surprised that not everyone could appreciate the elegance of what they had derived. "Based on this, if we can get a Naquada generator to produce a stable output of at least 108, which is doable for a short time, if not too advisable, I believe it may be possible to activate the secondary Chair and possibly bring it up to a sufficient operating level to access the City's security protocols."

"Have you checked if we can we reach one of the Naquada generators," said Weir, "and more importantly, do you have an exact location for this Chair yet?"

"We're in luck when it comes to the generator," Grodin said. "The nearest generator is separated from us by only one bulkhead. I've spoken to Captain Roberts and he's already got people working on cutting through it. He estimates he will be through in less than an hour. As for the location of the Chair…" He leaned over to the laptop and brought up a 3-D representation of the City. With the mouse pointer he indicated a point deep below the central hub of the City. "Here," he indicated. "This is partly conjectural; the architectural plans we'd pulled from the database a few weeks ago had the lower levels of the City only roughly blocked in. What we are sure about is that it's one of the oldest parts of the City, though we're not entirely certain how old. The section of archived material that Doctor Meidani found the references in we've been using dates back more than twenty thousand years, and she hasn't found any references to that part of the City more recent than eighteen thousand years ago, which means we've no way of being sure what condition things are in down there. And so far as I can recall, those sub-levels don't feature on the internal monitoring system."

Moving from where he had been sitting so as to get a better view of the laptop's screen, Sheppard studied it for a few moments and looked over at the others. "So if I understand this right, the plan is I go down to a part of the City we haven't explored yet, and which we've discovered we don't have reliable maps for, and while down there all I have to do is find a Control Chair which may or may not be there, and which may or may not work even if it _is_ there, and use it to cancel the City's security alert?"

McKay, Grodin and Zelenka exchanged glances. The idea had sounded so much better when they had been discussing it back in the laboratory. His enthusiasm only marginally dampened by the Major's sarcasm, McKay turned to him. "yes, that would be the plan."

"Oh wonderful," the Major grimaced. "So we've nothing to worry about. After all, we have a _plan_, don't we… What could possibly go wrong?"

Wisely no one answered.

"What's the current situation with regard to the evacuation?" Grodin asked, breaking the uncomfortable silence.

"At the moment we're going to have to be prepared to start evacuating non-essential personnel and equipment to the Alpha site," Weir stated. "Major Sheppard and his team have managed to find an access conduit to the Jumper bay and establish that the on board DHDs are still functioning. Captain Roberts estimates that it will take between two and three hours to get through the hangar bay door to allow a Jumper to get close enough to the Gate to dial it. Once we can get the Gate activated, we can send the alien power generator through to one of the uninhabited worlds we've come across such as M3S-427. The planet is a virtual desert so the generator should not be a risk to anybody there, now or in the future. Pass the word that I want volunteers for a skeleton crew to remain on Atlantis until an hour before the failsafe kicks in, and for everyone else who will be moving out to the Alpha site to be assembled in the Control Room with all the equipment we can take with us in ten hours. Major Sheppard, as soon as we've got the Naquada generator, I'll be wanting you and someone from the science team to see if you can find and activate this second Chair. Good plan or no, it looks like it's the only plan we've got to regain control over the City."

"Agreed. Rodney and I will be ready to go once the generator's been prepped," said Sheppard and turned to leave.

"What do you mean 'Rodney and I'," argued McKay, hurrying to catch up with the Major's brisk stride as fast as his injured ankle would allow. "Just hold on one moment, Major. Aren't you forgetting I get some input here with this whole 'agreement' issue…? Not wanting to be picky or anything, but I _am_ one half of this mission you've just gone and unilaterally volunteered us for."

Sheppard slowed and looked at him. "What are you telling me, Rodney? You honestly saying you think I should be getting someone else to go on this mission with me? Grodin? Zelenka? Can you tell me you think they, or anyone else here on Atlantis for that matter, would be able to get an abandoned piece of Ancient technology up and running anywhere near as well as you could?"

"Of course not," he said as if it were a fundamental universal law so obvious it hardly rated comment, then went on, "but it would have been nice to have been asked first."

A crooked smile crept over Sheppard's face. "Doctor McKay, can I interest you in a risky, possibly futile attempt to find the right doohickey to turn off Son-Of-Hal here and save the City?"

"You know, Major, when you think about it, that's a fairly inappropriate reference, and besides, I'm not sure a Control Chair can reasonably be described as a 'doohickey'…"

"Rodney..."

"If you think about it, aren't doohickies generally considered to be small?"

"Rodney…" Sheppard repeated more insistently.

"What?" McKay paused. "Oh yes, the whole saving-the-City thing. Comes down to me again, naturally. Because as you correctly point out, I _am_ the best man for the job."

"Yes, Rodney," the Major agreed calmly. "Of course, Rodney. Whatever you say, Rodney."

"Hey!"

Back in her office Weir could hear them still bickering as their voices faded from earshot; her two best problem solvers, gleefully sniping at each other like contrary teenagers. She allowed herself a small smile. Everyone in the room had known McKay would go despite his protests: complaints notwithstanding, the Canadian had always come through for them.

A little over an hour later Weir watched them leave. Equipped as if for an offworld mission, and carrying tools and the Naquada generator, Sheppard and McKay headed off for the stairs that were their only way down into the depths of Atlantis.

"Be safe!" she whispered.

o0o


	8. Chapter 7

**Chapter 7**

_I'd always hated swimming, hadn't I? _

McKay thought for a while, not a little confused, wondering what might have prompted such an odd observation. Memory drifted back piecemeal: he remembered sudden deafening noise, darkness, the impact of water, trying to swim, twisting and turning helplessly carried along by the flood, trying to work out which way was up. He remembered something hitting his head, a burning in his lungs, his vision lightening from black to a swirling red before settling on a dull, unremarkable grey.

He coughed abruptly, wincing at the tightness that seemed to have settled somewhere deep in his chest, then inhaled. _Oh, bad move._ He coughed again, then retched. Instinct urged him from his prone position to roll onto his side as he spat out the foul tasting liquid that he figured he had at some point swallowed. He sat up, fighting back an unpleasant surge of vertigo and renewed pounding from his aching head to look around. It was not quite pitch black, he decided, but not far from it. A hint of luminescence painted solid planes that had to be walls, floor and ceiling, but it was sufficient to distinguish vertical from horizontal, if not enough to see by. He reached out and let his fingers trace faint luminescent lines down the nearby wall, noting the moisture there. A shiver ran through him and he hugged himself for warmth.

_Oh God, I nearly drowned! _ Panic brought the rush of memory back full force: the endless flights of stairs leading downwards, deep into the City's sub-levels; finding the blocked door barring their way; Sheppard and his damned C-4; a moment's terrified realisation before the unstoppable wall of water slammed into them…

Sheppard! "Major!" he tried to shout, but it came out as little more than a strangled croak that dissolved into another bout of coughing. Fumbling hands pulled the canteen from its carry pouch and thumbed it open. He gargled, spat and finally drank a few gulps. "Major!" he tried again, slotting the canteen back in place. A cursory look round from his seated position revealed no light. There was not even a flicker that might have been from the flashlight he had carried with him, so he figured if it was nearby, it was apparently broken. He reached into an inner pocket of his vest, found the tiny penlight he had stashed there and switched it on.

The light was barely enough to read by, but it made him feel better and he felt a glimmer of amusement as he recognised the illogicality of it. The beam from the flashlight reached no more than ten or fifteen feet – all but useless for searching – so he listened instead. He heard the dripping of the water as it drained from the walls, and further off he could hear an occasional splash, receding into the distance.

"Major!" he yelled again, the word slowly echoing into silence down endless corridors stretching away from him. He listened again. The dripping continued, regular but gradually slowing in pace; the sound of distant splashing faded into inaudibility and was gone.

But there was something else. A moan? He turned, trying to work out where it had come from. The faintest sounds echoed deceptively in these corridors. He heard it again, close by, he was sure. The dim beam of his penlight picked out a lump on the floor of the passage. He crawled over towards it, grimacing at the slick feel on his hands of the stinking mud that covered the floor, left behind by the flood waters.

He neared the unmoving mud-covered figure. The darkness of the silt seemed to absorb whatever light hit it, so it revealed no more than the figure's outline. He hunkered down about ten feet away and studied it. To his gaze it looked wrong, twisted. McKay dreaded to think what terrible damage could have been inflicted on a human body to make it so misshapen. "Major!" he hissed urgently.

The figure made no move, no reply.

Worry for his friend's welfare overtook caution and he moved closer, close enough that even the dim light he had began to reveal details: details such as the fact that to his utter relief it was not Sheppard. Further examination convinced him it was not even human, it looked more like a big, pale-furred vaguely anthropomorphic otter.

He leaned forward to get a better look, his eyes taking in details of its shape. And while he was on the subject of details, were those _teeth_ marks he saw cut into its belly…?

"Yeeargh!" McKay yelped in horror, unable to stop himself, and blanking the stab of pain from his ankle he rapidly crab scuttling backwards into the opposite wall. The penlight dropped into the mud leaving only a faint glow to reveal its location.

Echoes of McKay's cry faded off into the distance and silence took over once again. Finally, refusing to be scared off by a corpse, and deciding he needed light more than he needed to pander to his squeamishness, he scrabbled through the mud for the penlight and wiped the mud from it as best he could, grateful for the accuracy of the manufacturer's apparently not quite so hyperbolic claims of durability and water resistance.

"Rodney?" came a not too distant cry, soon accompanied by a lightening of the oppressive dark appearing from a side corridor.

"Major!" McKay called back in acknowledgement, deciding to attribute any slight shrillness in his voice to a perfectly understandable relief at the survival of his friend and colleague.

The light bobbed around the corner, for an instant dazzling McKay until its focus was quickly shifted to illuminate the ceiling overhead. "You okay, McKay?" Sheppard asked, his gaze going up and down the mud covered physicist, checking for any obvious injury.

McKay coughed and spat. "Oh, just peachy. Aside from having swallowed several gallons of foul, probably disease ridden water, found a disgusting, half eaten corpse and almost cracked my head open, I'm fine!"

In the glow of the flashlight attached to his P-90 Sheppard could see the glaze of blood covering one side of McKay's face, the red of the blood paler than the surround grime. Moving cautiously he reached into a pouch on his vest and pulled free a field dressing. "Better get that cut on your head cleaned up," he said casually, not wanting to further alarm the already jittery Canadian. "Any headache? Nausea? Double vision?"

Any answer McKay might have made was lost in a sudden bout of coughing that ended with him turning aside to spit out a gob of phlegm. Sheppard took the opportunity to pull out his canteen and splash some water over McKay's head, washing away the worst of the blood and mud, then wrapping the bandage around it.

"How bad?" McKay eventually managed.

Sheppard forced a reassuring smile. "Doesn't look too bad: not more than a shallow cut," he hedged. "I just don't want to risk it getting any dirtier than it has to."

"I guess that makes sense," McKay said, managing an abortive nod before the stab of pain in his head announced that sudden head movements were a bad idea. Sheppard saw the wince and mutely handed over two pills from the small bottle of Tylenol he carried. McKay took them and swallowed them dry.

"Rodney, you good to go?" the Major asked.

Using the wall as support, McKay carefully got to his feet, leaning against it for a few moments as the wave of nausea subsided. "I really hope after that little swim you still have the Naquada generator," he muttered.

"Oh yeah," Sheppard answered in return and started walking back toward the remains of the blocked door he had needed to use the C-4 to open. McKay hobbled after him, giving the otter creature's corpse a wide berth, though favouring it with a worried look at the size of the gaping wound on its belly.

"So, you think it's still down here?" he asked.

"Hm?"

"The thing with the teeth," McKay went on. "The really _big_ teeth! From the state of it, that otter thing couldn't have died too long ago, so it makes sense that whatever it is might still be around."

"Hm," Sheppard replied with weary disinterest.

"What if it's amphibious?" he mused. "The dead thing was mammalian – I think – so maybe whatever killed it is too, and it doesn't need water to survive. Hey, it could still be down here with us!"

He waited for a reply, but none was forthcoming. Surprised by such a lack of response from a man who would normally have come back with some kind of snarky reply, McKay looked more closely at the figure in front of him. Sheppard's usually easy gait was now more of a hunched over trudge, and while the P-90 was held firmly in his right hand, instead of supporting it, the left arm was tucked in, pressing into his side.

While they backtracked to the torn remains that had been the blocked bulkhead door Sheppard had needed to use explosives to open, McKay noted with concern the noticeably unsteady way the Major walked. When they reached the bulkhead, he watched as Sheppard took a breath as if steeling himself before crouching down to climb through the hole in the centre that the blast and the subsequent out rush of water had left – though at the time neither had guessed the section might have been flooded. McKay noted the stiffness of his movements, heard the barely stifled gasp of pain, and concluded that Sheppard too had not escaped injury from the flood surge.

Sensing he was being watched, the Major looked up and saw the concerned if unspoken question in McKay's assessing gaze. "I bumped into one of the support pillars," he explained with a crooked, unconvincing grin. "Bruised a couple of ribs, that's all. I'll be okay."

If he heard McKay's answering snort of disbelief and muttered comments about the mule-headed stubbornness of certain Air Force Majors, he chose not to respond but instead lead the way further into the depths of the City.

o0o


	9. Chapter 8

**Chapter 8**

The corridors continued on, stretching away into the dark, relieved only by an occasional surviving lamp set into one or other of the walls that shed dim, blue tinged light across the silt covered corridor. The corridors were on a smaller scale than they were familiar with, lacking the bright airiness of their counterparts in the City above. Instead of clean geometric lines, the corridors this deep looked more organic in their architecture. As they walked onwards, they vaguely noted that any control panel or decoration they came across was an intertwined series of baroque curls, all now stained and blackened by the pervasive mud, and all dark and dead.

Hours passed. Their pace slowed as McKay's hobble became more and more pronounced and he found himself increasingly having to use the wall for support. More than once as they came across stairs or hallways, he had to reluctantly lean on Sheppard for assistance but each time struggling to put as little weight as he could on a friend he knew to be more badly hurt than he would admit. But finally they found what they had been searching for: a large circular room with a high domed roof lit by dim blue light. In the centre of it, standing on a platform that raised it out of the worst of the mud was a Chair; larger and more ornately decorated than the others they had seen, but very definitely a Control Chair.

With a glance at his watch, Sheppard cautiously shucked his pack and handed the Naquada generator over to McKay who set it down next to the Chair. He took his own pack off, removed the box of tools he had brought with him and favouring his ankle he settled down next to the Chair and got to work.

"How long?" Sheppard asked, his breath frosting in the chill air.

McKay made to answer, but any word were lost as he broke into coughing, a horrible racking sound, but he managed to master his voice long enough to whisper: "not long," and he started connecting cables from the generator to the platform at the back of Chair.

A few minutes later he levered himself to his feet and stepped back. "Okay, try it now, Major," he suggested, waving him over.

Sheppard carefully eased himself into the Chair, leaned back and concentrated. The only other time he had tried this and McKay asked him to imagine their location in the galaxy, he had barely needed to think about it to cause the map to appear. "Nothing's happening, Rodney," he ground out, an unmistakeable edge of urgency in his voice.

"Not really too surprising. No one's used this thing in thousands of years," McKay rasped, coughing painfully in the foul, leaden air, the exhalation condensing into billowing clouds in damp bone-numbing chill. "And God alone knows how much of that time it's been underwater," he muttered almost as an afterthought.

Sheppard remained where he was, laid back in the reclined throne-like Chair, his hands resting on the wide arms, just as he had done once before – admittedly by accident on that occasion – back in Antarctica. This time however, the Chair was most definitely not co-operating. Even through the BDUs he wore, he could feel the cold of whatever metal the Chair was made from leeching away the scant warmth in his body. A loud clang coming from behind and to one side of the chair's bulk startled him and he twisted around abruptly, only to find McKay had dropped the panel he had pulled away to gain access to the interior in an attempt to discover what was stopping it from working.

The latter fumbled for a few minutes, blowing on cold numbed hands in an effort to get some feeling back into them, then paused and peered about abruptly from where he was crouched, the partially teased out tangle of cables and crystalline blocks running to the chair temporarily forgotten. "What was that?" he whispered urgently, scoping out the room as if he had not seen it properly before. The sudden movement nudged the headache he had been nursing to new levels. "Major? I _told_ you before. There's definitely something down here."

He reached down to the Beretta holstered at his hip, heard the nearby click of a P-90's safety being disengaged, and felt rather than saw Sheppard's gaze tracking his own, checking out the room then staring back down the dank corridor they had emerged from only minutes before. The vestigial blue tinged lighting that had survived the ages in the domed room did little to dispel the pervasive murk. "I don't see anything," Sheppard admitted quietly.

"You sure?" The doubt in his tone was clear. "It's probably hiding… waiting to leap out on us when we least expect it. God! I'm talking like we're in one of those appalling teen slasher movies: dim lighting, a couple of poor brainless idiots wandering around with flashlights, something slimy with huge teeth lurking in the dark…" McKay's brittle laughter did little to reassure his team-mate.

Sheppard levered himself upward, ruthlessly choking back the pained gasp the movement caused and peered again into the darkness. Like spokes of a wheel spreading out from the hub, the empty corridors stretched away. In the dark, beyond the range of their flashlights he could just make out the faint shimmers of phosphorescence that outlined their own footprints along the corridor they had come down tracking through the stinking ankle deep mud. The only sounds were the almost imperceptible drone of the Naquada generator they brought with them on standby and the slow, unending drip… drip… drip… echoing from far off.

They could not even hear the warble of the City's alarm any more. The absence left a strange gap after its being part of the soundscape for so long, but they were too deep now.

Time crawled by as they watched and waited. "There's nothing out there," Sheppard finally decided and carefully settled back into the chair, only too aware of the stabbing ache in his side.

McKay harrumphed, gave one last, dubious, look down the corridor but trusting the Major's conclusion he knelt to return his attention to the task at hand, too preoccupied to notice when Sheppard's gaze was drawn inexorably back to the surrounding corridors or the worried frown that slowly crept over his face.

"Dammit, Major, listen to me! You're not even tr--!" It was all McKay managed to say before his words were taken over by what had over the past few hours become to Sheppard a now increasingly familiar bout of dry, wheezing coughs. Getting half drowned had taken its toll.

From his place in the chair he opened his eyes a slit to sneak a concerned sidelong glance to where his companion was standing, watching him. He had known the physicist was pale – intellectually he knew the effects of exhaustion, cold and blood loss – but had not noticed earlier just how truly ashen he was. The ambient dimly flickering blue-tinged light lent his features a corpse-like pallor. _And that blood stained excuse for a bandage wrapped around his head doesn't help,_ Sheppard grimly admitted, berating himself once again for not doing his job better. _I'm supposed to be able to keep the scientific side of the expedition safe. Great job of it I've done so far today…_

McKay fought a few moments to catch his breath, all the while holding up a hand in a mute request for patience before finally managing to gasp, "just one minute more… There's something else I can try," and ducked down to continue tweaking the jury rigged connections he had made in the pile of silvery white spaghetti so recently wrenched from the innards of the chair. Heavier wires snaked from deep within the Chair's platform to attach to the Naquada generator. He paused awhile, unable to stop his mind drifting as he noted how the faint white luminescence of the cables looked so oddly pristine amongst the layers of dark, fetid silt that covered almost everything else in the room.

"Any time now, Rodney…" reminded a dry voice.

Sheppard's words nudged him from the fugue he had too easily slid into and wearily he dragged his attention back to the present to remake another connection. A momentary crackle of power echoed by a startled yelp from the physicist was followed by a wisp of smoke and yet more coughing that had Sheppard trying to lever himself out of the chair to check on McKay when a triumphant, if hoarse, voice halted him. "Ha! Got it! Try it now…" he said and flicked the switch on the generator.

Sheppard barely had time to settle himself back in the Chair when a ripple of _something…_ something huge, utterly implacable and impossibly ancient slammed into his mind. He tried to fight, to object, even to hide, but in the merest fraction of a second knew he might as well have tried to turn back the sea. The mote that was John Sheppard was swept away in the tide.

And Rodney McKay could only watch in horrified disbelief as his friend's form arched in the chair, hands clenching and unclenching, mouth open in a silent rictus of agony as skeins of angry blue-white energy danced across his skin.

"Oh no…" he whispered as he lunged for the tangle of cables.

o0o


	10. Chapter 9

**Chapter 9**

"Oh no…" McKay whispered as he lunged for the tangle of cables. He made to grab at a bundle of wiring looped around a crystal which he had only moments earlier reconnected, wanting to pull it free and break the circuit. As soon as he touched the wires, he yelped. Even that brief contact had felt like lines of fire were being drawn across his palm and he hissed in pain, teeth gritted, and pulled back cradling his hand against his chest but a glance upwards showed that Sheppard was still in trouble and McKay was the only one who could do anything to help him.

He looked at the Naquada generator, thinking to just turn it off, only to see flickers of the same energy dancing across its casing as well. Urgently, he scanned the room, looking for something to use before settling on the assortment of tools they had brought with them. With his good hand he scrabbled through the box, searching for one that was insulated. "No… no… no…" Tools were pulled out and just as quickly thrown aside. "Yes!" His hand landed on a pair of plastic handled wire cutters and shook them free. Jaw clenched in determination he stabbed them into the tangle of cables, twisted and savagely jerked his hand backwards, tearing them free. On the Chair Sheppard slumped bonelessly, like a puppet with its strings cut, the only movement the occasional involuntary twitch as overloaded neurons fired random messages through his body.

McKay's tremulous hand reached out, searching for the pulse in Sheppard's neck, sighing in relief when he found it. It was weak, fast, worryingly arrhythmic, but at least it was there.

He smiled weakly, the pounding of his own heart only now beginning to calm. _If John Sheppard had been killed through **my** ineptitude…_ It did not bear thinking about. Rodney McKay was aware he did not make friends easily, and if a few short months ago someone had told him that a snarky Air Force Major with really bad hair would have been at the head of that very short list, he would have laughed in their face.

An unaccustomed pang of worry laced with an uncomfortable degree of guilt nagged at him as he looked searchingly at Sheppard's unconscious form, checking for any obvious signs of new injury but finding none. He was unsure what damage the chair might have inflicted, but to his eyes it had looked like he was being electrocuted. He could not help but wince as he considered how much internal damage the Major's own convulsive movements might have inflicted upon himself given he knew the man already had at least one broken rib, however much he had tried to pass the injury off as something trivial, but there was nothing he could do about that. His gaze tracked to the mess of cabling spread over the platform the Chair stood on, mercifully clear of the filth on the floor, then to his watch. _Only a couple of hours to go… okay… no pressure, then…_

With a lack of histrionics that might have surprised some of his former colleagues, he dug out the field medical kit Beckett had insisted they take with them. A wry smile acknowledged the Scots Doctor's foresight. _Though, perhaps on reflection, it wasn't so remarkable_, McKay decided. _Our team does seem to spend an inordinate amount of time in the infirmary so Carson can get us patched up. _ He found the burn salve and unwrapped a light dressing. A few minutes of awkward work later he was finished, pulling the final knot tight between his teeth and his good hand. _No awards for neatness, _he felt forced to admit, _but it does the job._

He flexed the hand cautiously. It was uncomfortable, but now the salve had numbed the worst of the burning pain, at least he could still use it. He checked Sheppard's condition once more. The man's heart rate had steadied somewhat and the disconcerting twitching had faded, but despite the chill air he was warm, probably too warm to the touch. While he was taking his pulse again, a low groan gave him a stab of hope that he might be coming to. "Major?" he tried, his voice taut with worry. "Major Sheppard?"

Eyes flickered open and peered owlishly at him, shuttered in pain. "Rodney?" The word was hardly loud enough to even be termed a whisper.

"Yeah. Uh… sorry about that, Major," McKay said, looking away for fear of seeing the accusation he was sure he would find in the Major's gaze. "I think I'm going to need to recheck things here."

"Time?" Sheppard managed, as if fighting to wrench his jumbled thoughts into some semblance of order.

McKay took a deep breath, forced a grin and worked on smothering the cough that was nagging at the back of his throat. "Not to worry, Major. It's all under control. I'll have this sorted out in no time."

Sheppard's eyebrows crawled upwards in disbelief. He knew that particular McKay grin, that 'trust-me-everything's-fine-I-know-_exactly_-what-I'm-doing' grin when the reality was anything but. Over the months they had worked together on Atlantis, he had grown too familiar with it not to recognise it now.

Under Sheppard's entirely too knowing regard the grin faltered. "Okay, I'll need to take some time to run down some of these circuits. There are a number of differences between this and the other Chairs I'm familiar with. I don't want to risk making assumptions again," he said. The words: _because last time I tried that, it nearly killed you,_ went unspoken.

"Work quickly," Sheppard urged, his voice a pained whisper. "We're running out of time, Rodney."

"Thanks _so_ much for pointing that out," McKay grumbled as he started the delicate task of teasing apart the chair's mechanism. "I had no _idea_ we were on a schedule here."

"Just get it working, McKay" came the Major's quiet, terse response and in the laboured tone McKay could hear the effort it had cost the man to speak and the audible hitch in his breathing whenever he tried to take anything like a full breath.

At that he frowned, pausing in his work on having such proof of how much the chair had hurt the Major. It was so notably unlike him to let slide the opportunity for a snarky come back, even at the worst of times. He wanted to say something to him, to apologise, to offer reassurance, but try as he might, he could not find the right words and the moment passed. Knowing the right thing to say to comfort a friend in pain was something, he knew, that he was not particularly good at, and for a rare instant he keenly felt the lack. Then the habit of years took over from the unfamiliar impulse and he contented himself with concentrating his efforts on getting the chair repaired. Saving the day, he decided quietly, was so much easier than trying to talk to people.

With that thought in mind, he settled down to study the chair, mentally putting together the detail of its functioning in his mind. As he did, curiosity took over and everything else became slipped back to secondary importance. The racking cough was soon all but ignored; the weariness that had almost become a part of him faded into irrelevance and pain from injuries, new and old, was sidelined as his mind settled into the challenge of deciphering the logic underlying the function of this older, more perplexing version of the Control Chair.

He traced circuit after circuit, checked the power capacity of the cables and the condition of the embedded crystals which were still intact, always referring back to the schematics and diagrams of the Antarctica Chair he had downloaded onto his PDA. The more he discovered, the more a disturbing picture was taking shape in his mind. The last set of readings taken, he inputted the final string of numbers into the PDA and waited for the machine to process them. Moments later, a series of statistics scrolled across the tiny screen, confirming his suspicions. For once, he had truly hoped he was wrong.

An expression of appalled realisation crossed McKay's face as he read the last figures on the screen of his PDA, and he knew in that moment why the Ancients had abandoned this chair.

And with that knowledge, his fear for the maverick Air Force Major who somewhere along the way had become his best friend returned tenfold.

"Major," he began haltingly, "there's something you need to know…" The words tailed off as he tried to think through how best to describe his findings and the danger they revealed.

"Rodney…" The unutterable weariness that he heard in Sheppard's tone made McKay wince even as the Major urged him to continue. "Talk to me."

If Sheppard had at that moment looked at the Canadian, the glimmer of anguish that he might have caught in the man's face would surely have explained his silence and hinted at the reason behind it, but instead he remained still, laid back in the Chair, eyes closed conserving his energy while he tried to recover what remained of his strength.

"Right, um… it's about the Chair," McKay prevaricated clumsily. "We already knew it's different from the Antarctica Chair and the one that's upstairs. For a start, it's a lot older, maybe by thousands of years. The other two are essentially identical in their set up from what I can tell. This one's… not. It's much less sophisticated; almost crude by Ancient standards. Compared with this one, there's a lot of stuff that's in the other Chairs that's, well, different - really fundamentally different, if we're going to make an issue out of it. But what's vastly more relevant right now is there's a whole lot more stuff I've seen in the other Chairs that just isn't here," McKay paused in his rambling then went back to poking around in the innards of the platform the Chair stood on then continued talking. "I'm guessing it's probably why, according the data we pulled from the records, this Chair's got so much lower energy requirements than the others – fewer systems to power, so lower overall power requirement ."

Sheppard noted with detached interest that as McKay got more involved in the technicalities of his subject, some of the jitteriness ebbed from his voice. "And I need to know all this, why?" he pressed gently, trying to get McKay back on the subject before he got too carried away by the physics.

The interruption pulled him up short, and McKay continued, his voice quieter, less confident with only the merest hint of his usual snarkiness. "Well, it's kind of important because a lot of the stuff that's not here are things like primary and secondary energy buffers, the finesse control interfaces, that sort of thing."

"In _English_, Rodney," Sheppard muttered.

"Okay," McKay extricated himself from the Chair's innards to talk directly to the Major, "back when you were using the Antarctica Chair, you weren't actually directly telling the system what to do; it was more like you were giving instructions to the control interface built into the Chair, and to explain it in excessively simplistic terms, that was in a way acting like an intermediary, transmitting your directions to the Chair's operation system, then receiving data from the system and converting it before transmitting it back to you."

"So, what you're saying is sort of like it's easier driving a car with power steering than without?"

McKay winced. "If you're going to put it in even _more_ simplistic terms, I suppose at a pinch you could take that as a valid parallel, but given the differential we're talking about, a better simile would be to say it's more like the difference between a flying a single engine Cessna and a 747 with a broken hydraulic system," he amended absently. "But that's not the point. The one safety feature, the only thing here that kept the operator at even one remove from the huge amount of power running through the Chair was this regulator." He pulled free a cluster of once silvery wires, embedded in which were a couple of cracked, blackened crystals, and lifted it high enough that the Major might see it.

Wearily Sheppard cranked open his eyes and turned to look. "I'm going to go out on a limb here and guess it's not supposed to look like that?"

McKay let it drop back to eye level and sighed, studying the burned out component he held. "Oddly enough, no," he admitted, matching Sheppard's dry tone.

Then in a flat, far too controlled voice Sheppard asked the question McKay had known and dreaded he would ask given what was at stake, the question he dreaded having to answer. "But can you still make the Chair work?"

Responses flew through McKay's brain. _Not a chance! No way! What are you thinking? That's too idiotic a thing to even suggest! The first attempt we made was when what laughingly passed for a safety feature was still working, at least until the power surge hit it, and even so the attempt nearly killed you!_

He looked up, his gaze met Sheppard's and he saw in the Major's eyes his absolute comprehension of what he was asking McKay to do, mirrored by a determination frightening in its intensity.

"I can make it work," McKay promised.


	11. Chapter 10

**Chapter 10**

"I can make it work," McKay promised, ignoring the hollow feeling that had settled at the base of his stomach as he spoke words that he was sure would condemn his friend to death. He paused for a moment as if steeling himself, muttered a few quiet, distinctly uncomplimentary things about Ancient engineers and safety protocols, then mouth set in a grim line he returned to working on the Chair. But this time it was notably less easy to lose himself in the intricacies of the engineering as his mind kept going back to Sheppard. The better he had got to know the Major over their months on Atlantis, the more he had become alarmed by the man's frequently cavalier attitude towards his own wellbeing. Considering the problem intellectually, he could rationalise the Major's decision, but he knew all the rationalisation in the world would not stop his hands shaking as he worked through assessing and sorting out the damage.

This time it was only too easy to trace where the circuitry had failed. After their earlier abortive attempt to make the Chair work, the damage that had caused made the locations of decayed wiring easy to spot: they had been the ones to have been fried. From intact, apparently redundant areas McKay ruthlessly tore out lengths of the silvery cables and spliced them across the damaged sections. The few remaining undamaged crystals were moved around to replace their damaged counterparts, while a couple more crystals scavenged from one of the room's inactive door controls were linked together in a rough approximation of the regulator, and wired into the Chair.

The worst of the damage repaired or bypassed, he stopped to look at his work. It was not the most aesthetically pleasing bit of engineering he had ever put together, but as he traced every circuit in his mind, he knew it was the best he could manage. His gaze tracked to where Sheppard lay unmoving on the reclined Chair. "Major?" he said softly. Sheppard did not move. Alarmed McKay stepped closer, reaching out a hand to check for the pulse on his neck. Beneath his fingers the skin felt warm and paper dry, the pulse shallow and fast, but even at the touch Sheppard remained worryingly unresponsive. McKay recalled one of their earlier offworld missions together when he had accidentally bumped into the snoozing Major at night and barely a second later had found himself thrown to the ground, looking down the barrel of a P-90. "Major?" McKay repeated, shaking the shoulder carefully.

Sheppard awoke with a stifled groan, turned towards him and opened his eyes blearily. "Wha-- Rodney?"

The confusion he saw in the Major's eyes made McKay's heart sink. It looked to have been as he ahd feared: the damage done by the Chair's malfunction on top of the earlier injury looked to have taken more out of the Major than, as usual, he had been willing to admit. McKay could not see that there was any way Sheppard would be strong enough to able to control the Chair in his present condition.

In McKay's mind that left them with only one option; an option, if he was being honest with himself, he would really much rather not consider. If Sheppard was no longer strong enough to handle the stress of controlling the Chair, then he, McKay, would have to step in and do it. They were both exhausted, but of the two of them, he figured he was in better health than Sheppard, though probably not by much, he decided, wincing from the leaden pain that was settling in his chest.

"Rodney? How are we doing?"

McKay looked up to find Sheppard awake and thankfully more lucid than a few minutes earlier, his voice hoarse but still stronger than before. He even saw a glimmer of the man's trademark lopsided grin. But just as Sheppard had grown accustomed to McKay's obfuscations, McKay too saw beyond the surface, beyond the sense of confidence and wellbeing the grin was meant to communicate. He saw the tension in the jaw line, the touches of colour on the too pale cheeks, the fever bright glint in the eyes, and knew Sheppard was nowhere near as well as he was trying to pretend.

"Change of plans, Major," McKay announced, speaking the words that committed him to the course of action before he realised he had consciously decided on it. "I'm going to operate the Chair; you're going to take the gun and watch out for whatever is lurking in those corridors."

With a grunt of effort, Sheppard hauled himself upright in the Chair to look McKay in the eyes. "Not going to happen, Rodney," he said with quiet, implacable determination.

"Look, Major, do you really think I _want_ to do this?" Indignation crept into McKay's voice. "Don't be so boneheaded! Just a few minutes ago you were all but unconscious. Think of what might happen if you pass out when I've got the Chair powered up. On the chance you've forgotten what I was trying to explain earlier, it's going to be a lot harder work to use this Chair than the others. If you're not able to control it…" His voice tailed off, unable to speak the words.

"I know that Rodney," Sheppard answered quietly, "and that's why _I'm_ the one who's got to do it. It's not that I don't appreciate the gesture; I do." He smiled for a moment, then as quickly as it came the smile faded and he went on, his tone uncompromising. "But when it comes down to it, as far as this expedition goes, you've got to realise that I'm a lot more expendable than you are," he finished with a faint if wry grin and carefully manoeuvred himself back down in the Chair.

McKay watched him, a worried frown on his face as any relief he might have felt was swept away by the rising fear that he could not push aside. "Major, I…" He stumbled at an unaccustomed loss for words.

"Yeah, Rodney, me too," Sheppard answered, holding his gaze for a few moments. He offered one last smile, trying to fit into that single expression all the reassurance he meant to offer but no longer had time to, then closed his eyes and reached out to place his hands on the arms of the Chair.

McKay took a breath, gathering his courage, then reached over to the switch on the Naquada generator and flicked it on.

For a moment he thought nothing had happened. There was no sudden noise; no flare of blue white energy as before; no smell or crackle of burning; and mercifully no repeat of what he had most dreaded: the sight of Sheppard convulsing under the assault of the energy that powered the Chair, an image that still returned with terrible clarity whenever he closed his eyes.

"Is it…?" he started to say, then looked more closely at the Major and the words tailed off. He saw the hand nearest to him gripping the arm of the Chair with bone-crushing urgency, the knuckles white even under the pallor. Every muscle trembled almost imperceptibly, as if fighting to hold in position under too great a strain. Drops of perspiration beaded on his taut features, but it was the eyes that caught McKay's attention: they were half open, the pupils fully dilated, fixed and staring, but at what McKay could no more than guess.

o0o

_It was different this time._

_A sensation he distantly recognised as pain nibbled at the edges of his consciousness and then slipped free, swept away by…_

_Ocean?_

_The word for it did not exist, but he decided he had to call it something so ocean would suffice. On the edges of his mind he sensed something huge and protean obligingly shift to more closely match the concept._

_Then it rushed towards him and for a vertiginous instant he felt lifted and carried as if in an Atlantic swell, then the moment was gone._

_The darkness returned along with a remote but nagging sensation of discomfort, then that too was leeched away by the enveloping dark, warm and comfortable and safe like an old, familiar quilt. _

_Half remembered thoughts of something he knew he ought to be doing slid into his mind with soporific languor. _

_**Focus! **_

_Focus on what? He was not sure where the voice – if it had been a voice – came from, but he was certain he did not recognise it._

_**Remember!**_

_Remember what? Oh, wait. That was it! There was a mission, wasn't there? The memory drifted back, nudging away the cloying dark. An oddly disconnected sensation of pain teased at the edge of his mind, rising and falling as if swept along by the wash of ocean._

_Yes, there was a mission. He had to… There was something he had to do… The City! That was it: he was supposed to save the City!_

_As the thought crystallised in his mind, he felt something heavy sweeping into him, dragging him down. The darkness split and fragmented, falling away to reveal something else, unforgiving and relentless, surging towards him._

_He looked up as cold and vast ocean slammed into him._

o0o

Seconds crawled by without apparent change, then the body on the Chair shuddered violently as if trying to pull back from something. On Sheppard's face McKay could see a tense frown creasing the Major's forehead and even as he watched, a thin dribble of blood slowly trickled from one nostril.

o0o


	12. Chapter 11

**Chapter 11**

Seconds crawled by without apparent change, then Sheppard's body shuddered as if trying to pull back from something. Looking at the Major's face McKay could see a tense frown creep over his features and to his dismay, even as he watched, a thin dribble of blood trickled slowly from one nostril.

o0o

_Ocean, vast and relentless washed about him._

_The sense of warmth and comfort was gone as if it had never been, and like a drowning man he struggled for a surface that perhaps, was not even there. Pain no longer remote crawled and seared down every artery and vein._

_He would have screamed if he could only work out how._

_It would have been so easy to let go, to sink into blissful oblivion, but he had always been stubborn and he and pain were old acquaintances. He knew he could let it win, or if he could still muster the strength and determination, he could bend it to his will, use it to hone his focus._

_The ocean stilled and pulled back, fusing with the shapeless dark that bounded his consciousness. The tide of pain wavered and ebbed._

_Before his eyes a tiny, slowly rotating architectural image of a structure rippled into being, a domed room with a Chair at its innermost point. While he looked on, it grew; layers of newer structure accreting on the old; millennia rushing by as he watched raking towers growing as if organic things, and sideways extensions reaching away from the old core gradually crystallising into the familiar shapes of Atlantis' piers. _

_In his mind he saw countless motes and lines of colour fill out the structure: reds, blues, greens, and other colours he had never before seen and could not name. On some level he knew all of them, their meaning and significance._

_He tried to think, to remember, but the knowledge skittered away untapped._

_A dull ache deep in his chest demanded attention. The image of the structure blurred, colours merged and bleached into nothingness. By sheer force of will he wrenched it back into focus._

_INSTRUCTIONS?_

_Without language or script, the word settled easily into the forefront of his mind. He thought about how he might best convey his wishes._

_The ache in his chest solidified into an inexorable pressure, becoming ever heavier, and spreading down his left arm. On some level he dimly recognised it as a bad sign. The focus on the image wavered again._

_Fear for his friends crept into his thoughts, fear that he might not after all be able to do this, fear that without the refuge of Atlantis they would not long survive against the Wraith. Like he used the pain, he used the fear to give him the strength to drag the image back into focus._

_As he did so a second image flickered into existence before him: a translucent oval marked by the shape of a human palm._

_In his mind he reached out to touch it. He felt no sense of contact, but at his touch the oval flared briefly and vanished. Beyond it the image of the City shimmered once as if viewed through heat haze. Threads of light sped across it and through it, almost too fast to follow, highlighting and connecting location after location. The threads of light coalesced at a single point somewhere deep in the City where they swirled and faded. _

_INSTRUCTIONS RECEIVED._

_The words pushed their way through into his mind, shaking his fierce concentration. _

_Theease of it startled him. That's it? As simple as that?_

_INSTRUCTIONS RECEIVED AND IMPLEMENTED. PRESENT SECURITY CONDITION RESET TO LEVEL ONE - NORMAL._

_Relief washed over him. The images before him blurred, fragmented and vanished. This time he did not fight it. He had done what he intended, and that was enough. Strands of empty greyness seeped into his mind and he fell._

o0o

McKay watched helplessly as the blood trickled down Sheppard's face. The Major's breath came in shallow, irregular gasps as if he was fighting for every breath of air.

A change in pitch of the sound from the Naquada generator and the faint tang of burning in the air dragged his attention from Sheppard's plight. The monitor gauges on the generator were all solidly in the red and warning lights were flashing with insistent urgency. For an instant McKay regretted his decision to disconnect the audible alarms, only to decide a second later that given the output level he had required from the generator, they would probably have been more distraction than use.

Having little choice in the matter he lunged forward, lifted and twisted the main shutdown on the generator. Immediately the pitch of the whine dropped down the register and within seconds faded into silence. Just as quickly the flashing of the warning lights slowed and stopped and McKay smiled in relief.

The smile lasted until he looked at the Chair. The overstrung tension in Sheppard's body was gone; the Major lay unmoving in the Chair in an abandoned sprawl. But what immediately seized McKay's attention was the now far more noticeable smell of burning accompanied by a thin plume of smoke rising from somewhere within the Chair's bulk.

"Oh no, no, no… definitely not good," he muttered. For a moment he fidgeted, trying to decide on a course of action, then events took a hand and narrowed his options as he heard the distinctive crackle from deep within the Chair of a crystal fracturing.

Heedless of the tearing pain from his sprained ankle that protested the sudden movement, he grabbed for the Major and in a single convulsive heave dragged him clear of the Chair. He stumbled backwards, and unable to keep his balance or his footing in the slick mud, all he could do was try to direct their fall as far away from the Chair and platform as possible.

The two crashed to the ground some ten feet from the Chair. McKay glanced back, saw more smoke, denser now, pouring from the open panel at the base of the Chair, heard a rattle, a high tremolo from deep in the platform, faint at first but increasing in volume, and knew he had run out of time. Unable to get further away, he threw himself to the ground over Sheppard's insensible form, protecting him as best he could against the explosion he was sure was coming.

Whether it was by design, the peril honed instincts of an inveterate experimenter, or just by sheer dumb luck they hit the ground a fraction of a second before the Chair exploded. The analytical part of McKay's mind – the part often at odds with the pragmatist in him – catalogued the explosion, and decided that as such things went, it was almost subdued: more a sudden burn out than a true concussive blast. Then analysis was all but forgotten as superheated fragments of the Chair rained down on him. He winced and yelped, flinching away from one impact into another. He heard them hiss as they tumbled away and were quenched in the chill mud.

In less than a minute the worst was over. Behind them all that remained of the Chair was a broken, smouldering shell. A slight movement next to him compelled his attention. "Major?" he said, the word little more than an asthmatic gasp. There was no response. He sat up, leaned over him and gently shook his shoulder, calling out more loudly, "Major!"

Slowly, as if waking from a coma, Sheppard blinked a couple of times, then frowned trying to focus on McKay's face only inches from his own. "Hey, Rodney," he croaked, "you might want to give me some space. People will talk."

McKay snorted in relieved amusement, the snort made to slip into perhaps slightly hysterical laughter only to overtaken by a bout of coughing that had him curling up to try to ease the pain in his chest. He spat out phlegm, oblivious, unlike Sheppard, to the rust coloured specks embedded in it. He coughed again, took a swig of water and looked at the Major. "After all this, I really hope it worked," he said.

His eyes on the shattered remnants of the Chair, Sheppard nodded slowly. "Oh yeah. Don't want to do that again." He paused a few seconds, catching his breath. "I don't remember the details too well, but I _think_ it worked." With far more effort than it should have taken, he pushed himself to his feet, swayed there a few moments then abruptly sat back down, both hands clutching his side. "Ah, remind me not to do that again any time soon," he gasped.

McKay half staggered, half crawled over to lean against the nearest wall. "So, now what? Even if it didn't work, you're not going to be able to walk out of here," he paused as if considering something else: "and _I_ sure as Hell can't carry you. What say we just wait here? If it did work, I figure Elizabeth's sure to send someone after us when they discover the City's not going to sink. If not… Either way, shouldn't take too long." He gestured wearily towards the Naquada generator. "I suppose if they're coming, they can home in on that."

Moving carefully, his arm pulled tight against his side, Sheppard made his way to where McKay had propped himself up against the wall. He pulled over a good sized panel blown off the Chair when it had exploded and sat down on it. After a few seconds, McKay shrugged and joined him. It was better than sitting in the mud.

"You know, I like that plan Rodney," Sheppard murmured, leaning back against the wall before slumping gently against McKay, finally giving in to the pain and exhaustion he had spent the past hours determinedly ignoring. "That's a _good_ plan… And whatever happens, one way or another, it's definitely been interesting."

"Yeah. No question there…"

o0o

Many hours later, following the faint but distinctive signal of the quiescent Naquada generator, Lieutenant Ford and Teyla, heading a Search and Rescue team sent out on Weir's order finally found the two of them there: both mud covered, bloodied, unconscious, and still propped up against each other for mutual support.

o0o


	13. Chapter 12

**Chapter 12**

_**24 hours later…**_

Weir looked down at the unmoving forms of her expedition's Senior Military Officer and the Head of the scientific team lying in the infirmary in adjacent beds. The sense of relief she felt on hearing the news that they were both alive had been muted somewhat when she had seen them both being carried into the infirmary. Ford and Teyla, neither of whom had left the infirmary since they had brought in the missing half of their team stood next to her while around them the medical team bustled, still engaged in returning the infirmary to its normal operating status after the evacuation order.

"How are they, Carson?" Weir asked as Beckett approached.

"Given time and rest, they'll both be okay," the Scottish Doctor said quietly, not wanting to disturb his patients. He looked over at McKay lying in the nearest bed. The filthy bandages he had been sporting on head and hand when he had been carried in had been replaced by ones clean, white and infinitely more neatly tied. "Rodney's had a close scrape of it this go around. It seems he picked up a chest infection that was on the verge of slipping into full blown pneumonia. I think we've caught it in time and the antibiotics we've got him on should head that off, but he'll still need to take it easy for awhile. The head injury looked worse that it was: no real concussion but it bled a lot as head wounds do. The burns on his hand and back were nae too bad: most were fairly superficial and should heal cleanly enough. And all the walking and whatever that he's been doing has nae done his ankle a jot of good. He'll be off that for some weeks yet."

Beckett walked past McKay and over to the side of Sheppard's bed, looked at the readout on the ECG the Major was connected up to and sighed. "It's the Major's condition that's been worrying me more. He's got himself a couple of broken ribs which have shifted about some. There was a wee bit of internal bleeding, most likely caused by one or other of them moving about, but we've gone in and managed to clear that up. Right now, though, it's his heart that's got me concerned: if I didnae know better, I'd read that ECG he's hooked up to and say not so long ago the laddie's had a heart attack, but too many of his other symptoms are off for me to make that diagnosis which has made knowing how to treat his condition a wee bit problematic. I've ended up just treating the symptoms and the readout's better now than it was when he was brought in, so it looks like he's recovering from it, whatever it was. With that uncertainty, I don't want to use any more aggressive heart medications unless his condition takes a turn for the worse and I have to. He has nae woken up yet, but Rodney briefly came to a couple of hours back and said something about the Chair nae working as it should, so that may be to do with what's caused it." Beckett shrugged, at a loss when it came to the vicissitudes of Ancient technology. "How about everything else going?" he asked.

"Slowly getting back to normal," Weir replied. "The major repairs are mostly completed. The Naquada generator Major Sheppard and Doctor McKay borrowed should be usable after a thorough overhaul; we've lost too many of those already not to try to get this one back into working order. Doctor Zelenka and Captain Roberts have managed to get the Gate Shield back up and running in record time. And it would seem that in the process Captain Roberts has acquired an interesting, if somewhat specialised, Czech vocabulary," she smiled.

"Aye, and it's not just the Captain. That Sergeant Callaghan was down here not too long ago doing some of the engineering work. I do wonder what Radek is going to think when he hears 'do prdele' in a Geordie accent!"

They grinned at the thought. Zelenka's reaction would surely be something to see.

"Elizabeth?" came a faint, slightly querulous voice from McKay's bed.

A warm, genuine smile crossed her features as she went to his bedside followed by the others. "Good to see you awake, Rodney," she said, the sentiment echoed quietly, but no less heartfelt by Ford and Teyla.

McKay offered her a half smile in reply and looked around, recognising the depressingly familiar sight of Atlantis' infirmary. "I'm guessing this means it worked out then."

Weir nodded. "We were only a few hours from the deadline, then out of nowhere everything just came back on line so I figured you must have succeeded. I sent Lieutenant Ford and Teyla out to find you not long after."

"Major Sheppard, is he okay?" McKay asked, ill-concealed anxiety creeping into his voice.

"Aye," said Beckett, "a bit the worse for wear,. He's sedated right now, but with a bit of time he'll be okay. Now get some rest. You can talk more later," he promised, shooed the others out of the curtained off part of the infirmary and dimmed the lights a little. Ford and Teyla exchanged glances and settled into chairs nearby.

o0o

Later that night, nudged into awareness by the sounds of quiet conversation, Sheppard's mind slowly surfaced from the drugged twilight where it had been comfortably floating. He cranked open an eye to see Ford and Teyla lightly dozing in the infirmary chairs that he recalled from personal experience were apparently designed for something other than comfort. Beyond them on the next bed along he could just make out McKay's slumbering form, and noted with relief that he was not attached to too much of Beckett's equipment. From further off he heard the hushed voices of Weir and Beckett in muted discussion at the other end of the infirmary.

Their presence there was reassurance enough that despite everything, McKay's plan had actually worked and both City and expedition had once again beaten the odds and survived, more or less intact. John Sheppard smiled and drifted back to sleep, absently wondering as he did why he kept dreaming of ocean.

Fin

A/N: Well, that's it! A big "Thank You" to everyone who has taken the time to write a review. Your comments and encouragement over the past few weeks have been very much appreciated.

And as for the critter(s) Rodney was so worried about – although they didn't make an appearance in this fic, they're probably still down there… possibly awaiting their opportunity for when I next can find time to write!


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